P1054Development of Genomic Resources for Solanum chilense and Solanum sitiens
Tomasz J. Kurowski
,
Cranfield University, School of Energy, Environment, and Agrifood, Cranfield, United Kingdom
Pedro Fidalgo De Almeida
,
Cranfield University, School of Energy, Environment, and Agrifood, Cranfield, United Kingdom
Fady Mohareb
,
Cranfield University, School of Energy, Environment, and Agrifood, Cranfield, United Kingdom
Niranjan Shirgaonkar
,
Indian Institute of Vegetable Research, Varanasi, India
Deepika Singh
,
Indian Institute of Vegetable Research, Varanasi, India
Geetika Bhagwat
,
Indian Institute of Vegetable Research, Varanasi, India
Sarvesh Pratap Kashyap
,
Indian Institute of Vegetable Research, Varanasi, India
H. C. Prasanna
,
Indian Institute of Vegetable Research, Varanasi, India
Andrew Thompson
,
Cranfield University, School of Energy, Environment, and Agrifood, Cranfield, United Kingdom
Water use efficiency and drought resistance are very desirable traits for tomato and many other agricultural crops. The cultivated tomato has three known wild relatives, native to arid areas, which exhibit such traits. One of them,
Solanum pennellii, has already been well studied, and has an established body of genomic resources including a reference genome. The development of high-quality reference genome sequences for the two other relatives,
Solanum chilense and
Solanum sitiens, is the main objective of this project.
Variant mapping using paired-end 150 bp Illumina HiSeq2500 data was undertaken for Solanum chilense to facilitate the breeding of introgression, advanced backcross and recombinant inbred line populations. A pipeline for selecting robust SNPs in coding regions was developed and used to create a set of 70,000 markers. Subsets of these will be used for genotyping during population development and in creation of genetic maps to support genome assembly.
Paired-end 250 bp data for genome assembly was generated using a PCR-free library construction protocol, resulting in 220x coverage for S. chilense and 160x coverage for S. sitiens. Using k-mer analysis, the sizes and heterozygosity rates of both genomes were estimated.
Multiple assemblies were generated for the two genomes using different software, including SOAPdenovo2 and DISCOVAR de novo. The current quality metrics for these assemblies will be presented. The highest quality assembly will be selected for further development using data from other platforms, including PacBio RSII, to enhance scaffolding, gap filling, and chromosome anchoring.
